Chemical Effects in Biological Systems—Data Dictionary (CEBS-DD): A Compendium of Terms for the Capture and Integration of Biological Study Design Description, Conventional Phenotypes, and ‘Omics Data

Authors: Fostel, Jennifer¹; Choi, Danielle¹; Zwickl, Craig²; Morrison, Norman³; Rashid, Asif¹; Hasan, Atif⁴; Bao, Wenjun⁵; Richard, Ann⁵; Tong, Weida⁶; Bushel, Pierre R.⁷; Brown, Roger⁸; Bruno, Maribel⁷; Cunningham, Michael L.⁹; Dix, David⁵; Eastin, William⁹; Frade, Carlos¹⁰; Garcia, Alex¹¹; Heinloth, Alexandra⁷; Irwin, Rick⁹; Madenspacher, Jennifer⁷; Merrick, B. Alex⁷; Papoian, Thomas¹²; Paules, Richard⁷; Rocca-Serra, Philippe¹¹; Sansone, Assunta-Susanna¹¹; Stevens, James²; Tomer, Kenneth⁷; Yang, Chihae¹³; Waters, Michael⁷

Source: Toxicological Sciences, Volume 88, Number 2, December 2005 , pp. 585-601(17)

Publisher: Oxford University Press

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Abstract:

A critical component in the design of the Chemical Effects in Biological Systems (CEBS) Knowledgebase is a strategy to capture toxicogenomics study protocols and the toxicity endpoint data (clinical pathology and histopathology). A Study is generally an experiment carried out during a period of time for the purpose of obtaining data, and the Study Design Description captures the methods, timing, and organization of the Study. The CEBS Data Dictionary (CEBS-DD) has been designed to define and organize terms in an attempt to standardize nomenclature needed to describe a toxicogenomics Study in a structured yet intuitive format and provide a flexible means to describe a Study as conceptualized by the investigator. The CEBS-DD will organize and annotate information from a variety of sources, thereby facilitating the capture and display of toxicogenomics data in biological context in CEBS, i.e., associating molecular events detected in highly-parallel data with the toxicology/pathology phenotype as observed in the individual Study Subjects and linked to the experimental treatments. The CEBS-DD has been developed with a focus on acute toxicity studies, but with a design that will permit it to be extended to other areas of toxicology and biology with the addition of domain-specific terms. To illustrate the utility of the CEBS-DD, we present an example of integrating data from two proteomics and transcriptomics studies of the response to acute acetaminophen toxicity (A. N. Heinloth et al., 2004, Toxicol. Sci. 80, 193–202).

Keywords: Chemical Effects in Biological Systems (CEBS) Know; toxicogenomics study protocols; toxicity endpoint data; acetaminophen; phenotypic anchor

Document Type: Research article

DOI: http://dx.doi.org/10.1093/toxsci/kfi315

Affiliations: 1: LIMT Lockheed Martin Information Technology (LMIT), Research Triangle Park, North Carolina 27709; 2: Lilly Research Laboratory, Greenfield, Indiana 46140; 3: National Environmental Research Council (NERC), University of Manchester, Manchester M13 9PL, U.K.; 4: Alpha-Gamma Technologies, Inc., Raleigh, North Carolina 27609; 5: U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711; 6: U.S. National Center for Toxicogenomics Research (NCTR), Jefferson, Arkansas 72079; 7: U.S. National Center for Toxicogenomics (NCT), Research Triangle Park, North Carolina 27709; 8: Glaxo-SmithKline, Inc., Research Triangle Park, North Carolina 27709; 9: U.S. National Toxicology Program, Research Triangle Park, North Carolina 27709; 10: Xybion, Inc., Cedar Knolls, New Jersey; 11: The European Bioinformatics Institute (EMBL-EBI) Hinxton, Wellcome Trust Genome Campus, Cambridge CB10, U.K.; 12: U.S. Food and Drug Administration (FDA) Center for Drug Evaluation and Research, Rockville, Maryland 20857; and 13: Leadscope, Inc., Columbus, Ohio 43215

Publication date: 2005-12-01

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The mission of Toxicological Sciences, the official journal of the Society of Toxicology, is to publish premier peer-reviewed, hypothesis-driven, original research articles in all areas of toxicology. Toxicological Sciences Manuscript Central (ToxSci MC), our online submission system, is located at http://mc.manuscriptcentral.com/toxsci. ToxSci MC facilitates convenient uploading of original and revised manuscripts, as well as online review-ing and intercommunication between authors, editors, and reviewers.

Chemical Effects in Biological Systems—Data Dictionary (CEBS-DD): A Compendium of Terms for the Capture and Integration of Biological Study Design Description, Conventional Phenotypes, and ‘Omics Data

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